[Ecopd-commits] r80 - in branches/single-tree: . R man

[noreply at r-forge.r-project.org]

Author: regetz
Date: 2009-11-18 07:31:42 +0100 (Wed, 18 Nov 2009)
New Revision: 80

Added:
   branches/single-tree/R/genera.R
Modified:
   branches/single-tree/DESCRIPTION
   branches/single-tree/R/utilities.R
   branches/single-tree/man/genera.Rd
Log:
rewrote genera function as set of methods for phylo4 and phylo4com
objects; updated documentation accordingly


Modified: branches/single-tree/DESCRIPTION
===================================================================
--- branches/single-tree/DESCRIPTION	2009-11-18 06:27:58 UTC (rev 79)
+++ branches/single-tree/DESCRIPTION	2009-11-18 06:31:42 UTC (rev 80)
@@ -8,6 +8,6 @@
 Depends: methods, phylobase
 Description: A set of metrics and functions for combining ecological and phylogenetic information
 License: GPL
-Collate: phylo4com.R coerce.R utilities.R community.R pd.R aed.R iac.R pae.R simpson.R indices.R plots.R
+Collate: phylo4com.R coerce.R genera.R utilities.R community.R pd.R aed.R iac.R pae.R simpson.R indices.R plots.R
 LazyLoad: yes
 LazyData: yes

Added: branches/single-tree/R/genera.R
===================================================================
--- branches/single-tree/R/genera.R	                        (rev 0)
+++ branches/single-tree/R/genera.R	2009-11-18 06:31:42 UTC (rev 80)
@@ -0,0 +1,24 @@
+setGeneric("genera", function(x, ...) {
+    standardGeneric("genera")
+})
+
+setMethod("genera", c("phylo4"),
+  function(x) {
+    # From taxa names in tree, remove "_" and species name after
+    gsub("_.*$", "", tipLabels(x))
+})
+
+setMethod("genera", c("phylo4com"),
+  function(x, community) {
+    if (missing(community)) {
+        community <- communities(x)
+    }
+    doNotExist <- !community %in% communities(x)
+    if (any(doNotExist)) {
+        stop("one or more communities not found in x: ",
+            paste(community[doNotExist], collapse=", "))
+    }
+    g <- lapply(getSubtrees(x, community), genera)
+    names(g) <- community
+    return(g)
+})


Property changes on: branches/single-tree/R/genera.R
___________________________________________________________________
Name: svn:eol-style
   + native

Modified: branches/single-tree/R/utilities.R
===================================================================
--- branches/single-tree/R/utilities.R	2009-11-18 06:27:58 UTC (rev 79)
+++ branches/single-tree/R/utilities.R	2009-11-18 06:31:42 UTC (rev 80)
@@ -110,25 +110,6 @@
   return(phy)
 }
 
-##TODO method-ize this, adding method for phylo4, then calling that
-##method from this more complex phylo4com method
-# genera extractor
-genera <- function(phy, comm) {
-    if (missing(comm)) {
-        comm <- communities(phy)
-    }
-    doNotExist <- !comm %in% communities(phy)
-    if (any(doNotExist)) {
-        stop("one or more communities not found in phy: ",
-            paste(comm[doNotExist], collapse=", "))
-    }
-    # From taxa names in tree, remove "_" and species name after
-    g <- lapply(phy at subtrees[phy at metadata$comms[comm]], function(x)
-        gsub("_.*$", "", tipLabels(x)))
-    names(g) <- comm
-    return(g)
-}
-
 # community labels extractor
 communities <- function(phy) {
   names(phy at metadata$comms)

Modified: branches/single-tree/man/genera.Rd
===================================================================
--- branches/single-tree/man/genera.Rd	2009-11-18 06:27:58 UTC (rev 79)
+++ branches/single-tree/man/genera.Rd	2009-11-18 06:31:42 UTC (rev 80)
@@ -1,5 +1,9 @@
 \name{genera}
+\docType{methods}
 \alias{genera}
+\alias{genera-methods}
+\alias{genera,phylo4-method}
+\alias{genera,phylo4com-method}
 \title{Extract genus names}
 \description{
   Helper function to extract the genus names from phylogeny tip labels
@@ -7,11 +11,12 @@
   nomenclature.
 }
 \usage{
-  genera(phy, comm)
+  \S4method{genera}{phylo4}(x)
+  \S4method{genera}{phylo4com}(x, community)
 }
 \arguments{
-  \item{phy}{a \code{phylo4com} object}
-  \item{comm}{a vector of community labels; if missing, all communities}
+  \item{x}{a \code{phylo4com} object}
+  \item{community}{a vector of community labels; if missing, all communities}
 }
 \details{
   This is a simple function that assumes the tip labels of phylogeny
@@ -19,13 +24,15 @@
   whatsoever to check whether this is in fact the case.
 }
 \value{
-  A list of character vectors, one per community, containing the genus
-  portion of the tip labels, with element names corresponding to the
-  numeric tip node ID.
+  For \code{phylo4}, a character vector containing the genus portion of
+  the tip labels, with element names corresponding to the numeric tip
+  node ID. For \code{phylo4com}, a list of such vectors, one per
+  community.
 }
 \author{Jim Regetz (regetz at nceas.ucsb.edu)}
 \examples{
   data(weeds)
+  genera(weeds)
   genera(weeds, "A")
-  genera(weeds)
+  genera(phylo4(weeds))
 }